The maintenance of genetic variation in traits under natural selection is a long-standing paradox in evolutionary biology [1][2][3] . Of the processes capable of maintaining variation, negative frequency-dependent selection (where rare types are favoured by selection) is the most powerful, at least in theory 1 ; however, few experimental studies have confirmed that this process operates in nature. One of the most extreme, unexplained genetic polymorphisms is seen in the colour patterns of male guppies (Poecilia reticulata) 4,5 . Here we manipulated the frequencies of males with different colour patterns in three natural populations to estimate survival rates, and found that rare phenotypes had a highly significant survival advantage compared to common phenotypes. Evidence from humans 6,7 and other species 8,9 implicates frequency-dependent survival in the maintenance of molecular, morphological and health-related polymorphisms. As a controlled manipulation in nature, this study provides unequivocal support for frequency-dependent survival-an evolutionary process capable of maintaining extreme polymorphism.Colour-pattern polymorphism in guppies is limited to males and consists of irregular spots of several different structural (blue, green and purple) and pigment-based (yellow, orange, red and black) colours that occur on the body, caudal fin and dorsal fin (Fig. 1). The position, number, size and hue of the spots are highly heritable 5,10 , although the colour saturation (chroma) of orange spots can be influenced by diet 11,12 . Male colouration is highly polymorphic despite being subject to sexual and ecological selection. Female mating preferences usually favour males with the greatest area of orange, although the strength of that preference varies among populations 10,12,13 . Predators also exert selection on colour patterns; they preferentially prey upon males with brighter or more conspicuous colours 14,15 . Despite the apparently strong and directional selection within populations, colour patterns are so variable that any two males are easily distinguishable based on colour pattern alone, unless they are closely related 10 .Several mechanisms have been proposed to explain the maintenance of this extreme polymorphism 10,14 . Mate-choice experiments indicate that females preferentially mate with males bearing rare or novel colour patterns 16,17 . A trade-off (antagonistic pleiotropy) between male sexual attractiveness and offspring viability has also been reported 18 . Both processes could contribute to the maintenance of genetic variation in nature. However, experiments demonstrating these processes were conducted in laboratory environments, and it is not clear whether either process occurs in nature. Another process capable of maintaining polymorphism is a rare-morph survival advantage. This process has been implicated in the maintenance of colour polymorphism in some invertebrates 19,20 and vertebrates 21 , but it has not been tested in the highly polymorphic guppy system. We tested the hypothesis that ma...

Springsnails of the genus Pyrgulopsis are the most diverse group of freshwater gastropods in North America and current estimates show that Pyrgulopsis contains ~120 different species, many of which are at risk of extinction. Some factors contributing to their exceptional diversity include poor dispersal ability and extreme habitat specificity based on water availability, chemistry and depth. Most taxa exhibit high degrees of endemism, with many species occurring only in a single spring or seep, making springsnails ideal for studies of speciation and population structure. Here I present data from a survey of genetic variation at the mitochondrial gene cytochrome oxidase I from 37 populations and over 1000 individuals belonging to 16 species of Pyrgulopsis distributed throughout the lower Colorado River basin. High levels of interspecific sequence divergence indicate that Pyrgulopsis may have colonized this region multiple times beginning in the late Miocene (~6 Ma); earlier than previous estimates based on fossil evidence. Estimates of nucleotide diversity differ greatly among species and may reflect differences in demographic processes. These results are used to identify factors contributing to radiation of species in this region. The implications of this evolutionary history and genetic variation are discussed in relation to future management and conservation.

The completion of the Panamanian Isthmus is one of the greatest natural experiments in evolution, sending multiple species pairs from a broad range of taxonomic groups on independent evolutionary trajectories. The resulting transisthmian sister species have been used as model systems for examining consequences that accompany cessation of gene flow in formerly panmictic populations. However, variance in pairwise genetic distances of these "geminates" often exceeds expectations, seemingly conflicting with the assumption that separation of populations was contemporaneous with the final closure of the Isthmus. Multilocus datasets and coalescent-based analytical methods can be used to estimate divergence times while accounting for variance in gene divergence that predates isolation, thus removing the need to invoke unequal divergence times. Here we present results from Bayesian analyses of sequence data from seven nuclear and one mitochondrial marker in eight transisthmian species pairs in the snapping shrimp genus Alpheus. Divergence times in two species pairs were shown to occur much earlier than the Isthmus final closure, but much of the variance in pairwise genetic distances from cytochrome oxidase I (COI) was explained when ancestral polymorphisms were accounted for. Results illustrate how coalescent approaches may be more appropriate for dating recent divergences than for estimating ancient speciation events.

Divergent natural selection driven by competition for limited resources can promote speciation, even in the presence of gene flow. Reproductive isolation is more likely to result from divergent selection when the partitioned resource is closely linked to mating. Obligate symbiosis and host fidelity (mating on or near the host) can provide this link, creating ideal conditions for speciation in the absence of physical barriers to dispersal. Symbiotic organisms often experience competition for hosts, and host fidelity ensures that divergent selection for a specific host or host habitat can lead to speciation and strengthen pre-existing reproductive barriers. Here, we present evidence that diversification of a sympatric species complex occurred despite the potential for gene flow and that partitioning of host resources (both by species and by host habitat) has contributed to this diversification. Four species of snapping shrimps (Alpheus armatus, A. immaculatus, A. polystictus and A. roquensis) are distributed mainly sympatrically in the Caribbean, while the fifth species (A. rudolphi) is restricted to Brazil. All five species are obligate commensals of sea anemones with a high degree of fidelity and ecological specificity for host species and habitat. We analysed sequence data from 10 nuclear genes and the mitochondrial COI gene in 11-16 individuals from each of the Caribbean taxa and from the only available specimen of the Brazilian taxon. Phylogenetic analyses support morphology-based species assignments and a well-supported Caribbean clade. The Brazilian A. rudolphi is recovered as an outgroup to the Caribbean taxa. Isolation-migration coalescent analysis provides evidence for historical gene flow among sympatric sister species. Our data suggest that both selection for a novel host and selection for host microhabitat may have promoted diversification of this complex despite gene flow.

Extirpated organisms are reintroduced into their former ranges worldwide to combat species declines and biodiversity losses. The growing field of reintroduction biology provides guiding principles for reestablishing populations, though criticisms remain regarding limited integration of initial planning, modeling frameworks, interdisciplinary collaborations, and multispecies approaches. We used an interdisciplinary, multispecies, quantitative framework to plan reintroductions of three fish species into Abrams Creek, Great Smoky Mountains National Park, USA. We first assessed the appropriateness of habitat at reintroduction sites for banded sculpin (Cottus carolinae), greenside darter (Etheostoma blennioides), and mottled sculpin (Cottus bairdii) using species distribution modeling. Next, we evaluated the relative suitability of nine potential source stock sites using population genomics, abundance estimates, and multiple-criteria decision analysis (MCDA) based on known correlates of reintroduction success. Species distribution modeling identified mottled sculpin as a poor candidate, but banded sculpin and greenside darter as suitable candidates for reintroduction based on species-habitat relationships and habitats available in Abrams Creek. Genotyping by sequencing revealed acceptable levels of genetic diversity at all candidate source stock sites, identified population clusters, and allowed for estimating the number of fish that should be included in translocations. Finally, MCDA highlighted priorities among candidate source stock sites that were most likely to yield successful reintroductions based on differential weightings of habitat assessment, population genomics, and the number of fish available for translocation. Our integrative approach represents a unification of multiple recent advancements in the field of reintroduction biology and highlights the benefit of shifting away from simply choosing nearby populations for translocation to an information-based science with strong a priori planning coupled with several suggested posteriori monitoring objectives. Our framework can be applied to optimize reintroduction successes for a multitude of organisms and advances in the science of reintroduction biology by simultaneously addressing a variety of past criticisms of the field.

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Many aquatic species have become endangered because of the elimination and fragmentation of their habitat, human alteration of the environment, and introduced species. New applications and insights from genetic studies of endangered species are being used to formulate management plans to prevent extinction of endangered taxa. Here we discuss three applications of genetic techniques to the conservation of endangered aquatic species in the desert Southwest, USA. First, we discuss estimation of long-term effective population size in three endangered big-river fishes, bonytail chub (Gila elegans), humpback chub (G. cypha) and razorback suckers (Xyrauchen texanus), of the lower Colorado River. For all three species, the current census number is much smaller than the estimated effective population size in which these species evolved. Second, we discuss the determination of species, ESUs, and MUs in the endangered Sonoran topminnow. Molecular genetic data show that the Gila Aquatic Sciencesand Yaqui topminnows are different species. Experimental examination of pre-mating and post-mating reproductive isolation demonstrates that some reproductive isolation has already developed between these two species. Finally, springsnails (Pyrgulopsis) of the lower Colorado River basin exist only in remote and isolated springs. Examination of molecular variation generally supports the morphological designation of 16 different species, although a few species have several ESUs. There does not appear to be a correlation of genetic and geographic distance between species, suggesting that they are quite old. These genetic studies provide insight into the conservation of these rare aquatic species. Although mitigating ecological factors may be most significant in preventing extinction, genetic studies can provide the evolutionary context for endangered species and identify what units are most in need of conservation.

The taxonomy of the snapping shrimpAlpheus cristulifronsRathbun, 1900, previously reported from the eastern Pacific and western and eastern Atlantic, is reviewed based on molecular data (COI), morphology and colour patterns. Three species are recognized in theA. cristulifronsspecies complex.Alpheus cristulifrons sensu strictois restricted to the western Atlantic, ranging from Florida and the Caribbean Sea to southern Brazil. The eastern PacificA. cristulifrons sensuKim & Abele, 1988 corresponds toA. utriensisRamos & Von Prahl, 1989, ranging from the Gulf of California to Colombia; this species can be separated fromA. cristulifronsby the absence of balaeniceps setae on the male minor chela and the presence of bands on the antennular and antennal flagella. The eastern AtlanticA. cristulifronssensuCrosnier & Forest, 1966 is described asA. xanthocarpussp. nov. based on recently collected material from the island of São Tomé in the Gulf of Guinea; this species differs fromA. cristulifronsby the posteriorly more extending rostral carina and the presence of conspicuous yellow spots on the carpus and chela of the second pereiopod. Molecular data suggest thatA. utriensisis the eastern Pacific sister clade to the amphi-Atlntic clade that includesA. cristulifronsandA. xanthocarpussp. nov.